TFs regulating LINC01409 0 TFs

Transcription factors with Perturb-seq knockdown data for LINC01409. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = LINC01409 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to LINC01409

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of LINC01409, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr1:904,256–904,920	126.0 kb	Distal (>10kb) Multiome	590
chr1:923,612–925,339	145.1 kb	Distal (>10kb) Multiome	500
chr1:939,835–943,080	163.1 kb	Distal (>10kb) Multiome	864
chr1:959,035–960,017	180.5 kb	Distal (>10kb) Multiome	622
chr1:960,291–961,429	182.0 kb	Distal (>10kb) Multiome	552
chr1:975,960–976,521	197.4 kb	Distal (>10kb) Multiome	476
chr1:998,350–1,000,999	221.5 kb	Distal (>10kb) Multiome	1047
chr1:1,001,349–1,002,099	223.2 kb	Distal (>10kb) Multiome	646
chr1:1,005,015–1,005,702	226.5 kb	Distal (>10kb) Multiome	532
chr1:1,019,142–1,021,414	240.8 kb	Distal (>10kb) Multiome	707
chr1:1,032,438–1,034,753	254.4 kb	Distal (>10kb) Multiome	475
chr1:1,040,071–1,041,597	262.2 kb	Distal (>10kb) Multiome	410
chr1:1,058,856–1,060,114	280.7 kb	Distal (>10kb) Multiome	609
chr1:1,068,556–1,069,991	290.4 kb	Distal (>10kb) Multiome	577

Genome Browser

Genomic view of the LINC01409 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.